> I was looking at galaxy/dist/tools/sr_mapping/bowtie2_wrapper.* and it
> does not seem to challenging to add another field where a user could
> specify some integer value that we simply pass to the the <command>
> tag in the xml file.
> Would this be the correct way to go about this?

Yes, this is correct; the -X or -I option are good examples of using integer 

The Bowtie2 wrapper has never been fleshed out; if you do decided to add 
options, please consider submitting a pull request so that others can benefit 
from your work as well.

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